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RPKM
•
reset
0
votes
0
replies
1.6k
views
Tutorial:
Read data file containing both counts and annotation into edgeR
rpkm
edgeR
featureCounts
17 months ago
Gordon Smyth
52k
1
vote
4
replies
5.4k
views
Conversion from FPKM,RPKM to tpm
DESEQ2
fpkm
rpkm
tpm
3.4 years ago
Sandhiya
• 0
9
votes
10
replies
8.7k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization
edgeR
RPKM
updated 23 months ago by
Chris
▴ 20 • written 4.3 years ago by
anikng
▴ 10
1
vote
5
replies
1.7k
views
bug in "dispersion" argument in edgeR - rpkmByGroup
edger
rpkm
updated 5.7 years ago by
rosehahn8583
• 0 • written 5.7 years ago by
dario.beraldi
• 0
7
votes
3
replies
4.0k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
kushshah
▴ 10
2
votes
1
reply
1.6k
views
Bioconductor with RPKM counts or Raw counts
singlecellexperiment
rpkm
normalization
qc
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
kushshah
▴ 10
1
vote
1
reply
1.3k
views
Generating RPKM data from dds (DESeq2 pipeline)
deseq2
dds
RPKM
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
harry.horsnell.17
• 0
32
votes
16
replies
20k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport
deseq2
TPM
RPKM
rnaseq
updated 6.8 years ago by
luxeredias
▴ 20 • written 8.6 years ago by
tangming2005
▴ 200
3
votes
1
reply
1.4k
views
RMS question in MEDIPS
RMS
RPKM
MEDIPS
updated 7.0 years ago by
Lukas Chavez
▴ 570 • written 7.0 years ago by
enrique.yeh
▴ 10
2
votes
14
replies
8.8k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 24 months ago by
Chris
▴ 20 • written 7.5 years ago by
Biologist
▴ 120
3
votes
2
replies
1.9k
views
AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub
roadmap project
rpkm
data.frame
8.4 years ago • updated 8.3 years ago
wcstcyx
▴ 30
4
votes
2
replies
5.8k
views
How to run the rpkm function of edgeR
edger
rpkm
updated 9.0 years ago by
Aaron Lun
★ 28k • written 9.0 years ago by
Gary
▴ 20
4
votes
10
replies
5.8k
views
Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm
gene length
count matrix
edgeR
rsubread
9.3 years ago
AB
▴ 110
4
votes
1
reply
2.6k
views
Get source code for rpkm() function in edgeR
edgeR
rpkm
source
code
updated 9.9 years ago by
Martin Morgan
25k • written 9.9 years ago by
thibault.lorin
▴ 10
7
votes
4
replies
2.9k
views
Gene expression between two copies of same gene:use counts or RPKM or FPKM?
count
rnaseq
rpkm
fpkm
edgeR
updated 9.9 years ago by
Gordon Smyth
52k • written 9.9 years ago by
thibault.lorin
▴ 10
3
votes
3
replies
7.6k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg
rna-seq
rpkm
updated 9.9 years ago by
b.nota
▴ 370 • written 9.9 years ago by
Yue Zhao
• 0
0
votes
5
replies
2.9k
views
count tables created with easyRNASeq and the rpkm() function from edgeR
easyrnaseq
edger
rpkm
updated 10.0 years ago by
Nicolas Delhomme
▴ 320 • written 10.0 years ago by
Sylvain Foisy
▴ 80
4
votes
4
replies
22k
views
edgeR rpkm function
edger
rpkm
updated 23 months ago by
Gordon Smyth
52k • written 10.0 years ago by
Makis Motakis
▴ 30
3
votes
2
replies
16k
views
how to calculate gene length to be used in rpkm() in edgeR
RNASeq
edgeR
rpkm
updated 22 months ago by
Gordon Smyth
52k • written 10.8 years ago by
shirley zhang
★ 1.0k
2
votes
1
reply
1.8k
views
Shoud I use "aligned reads" or total reads (aligned + unassigned) to the RPKM value?
rnaseq
R
rsubread
rpkm
updated 10.3 years ago by
James W. MacDonald
68k • written 10.3 years ago by
gustavoborin01
• 0
20 results • Page
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Answer: SingleR with multiple single cell references
by
Aaron Lun
★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies
by
ATpoint
★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
Answer: To count or not to count multi-overlapping reads?
by
Gordon Smyth
52k
> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…
Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Votes
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